A fluorescence-based screening assay for DNA damage induced by genotoxic industrial chemicals.

A rapid screening assay to detect chemically-induced DNA damage resulting from exposure of surrogate DNA to genotoxic compounds is reported. This assay is based on changes in the melting and annealing behavior observed for damaged DNA. Exposure of calf thymus DNA to genotoxic industrial chemicals reduced the extent to which the DNA annealed as measured using a double strand DNA selective fluorescent indicator dye. Formaldehyde, acrolein, crotonaldehyde and bromoethane showed the most prominent effects, chloroacetone and allylamine exhibited lesser effects, and acryrlonitrile showed no statistically significant assay response. The assay response for formaldehyde and crotonaldehyde were measured over the concentration range of 10-100 mM and 50-300 mM, respectively. This assay showed little response for the cytotoxic compounds phenol, cyclohexane and toluene but was sensitive to the effects of DNA damaging compounds such as mitomycin C and glutaraldehyde.

Recent advances in biosensor techniques for environmental monitoring.

Biosensors for environmental applications continue to show advances and improvements in areas such as sensitivity, selectivity and simplicity. In addition to detecting and measuring specific compounds or compound classes such as pesticides, hazardous industrial chemicals, toxic metals, and pathogenic bacteria, biosensors and bioanalytical assays have been designed to measure biological effects such as cytotoxicity, genotoxicity, biological oxygen demand, pathogenic bacteria, and endocrine disruption effects. This article is intended to discuss recent advances in the area of biosensors for environmental applications.

KIF1D is a fast non-processive kinesin that demonstrates novel K-loop-dependent mechanochemistry.

The KIF1 subfamily members are monomeric and contain a number of amino acid inserts in surface loops. A particularly striking insertion of several lysine/arginine residues occurs in L12 and is called the K-loop. Two recent studies have employed both kinetic and single-molecule methods to investigate KIF1 motor properties and have produced very different conclusions about how these motors generate motility. Here we show that a hitherto unstudied member of this group, KIF1D, is not chemically processive and drives fast motility despite demonstrating a slow ATPase. The K-loop of KIF1D was analysed by deletion and insertion mutagenesis coupled with characterization by steady state and transient kinetics. Together, the results indicate that the K-loop not only increases the affinity of the motor for the MT, but crucially also inhibits its subsequent isomerization from weak to strong binding, with coupled ADP release. By stabilizing the weak binding, the K-loop establishes a pool of motors primed to undergo their power stroke.

Biosensors for direct determination of organophosphate pesticides.

Direct, selective, rapid and simple determination of organophosphate pesticides has been achieved by integrating organophosphorus hydrolase with electrochemical and opitical transducers. Organophosphorus hydrolase catalyzes the hydrolysis of a wide range of organophosphate compounds, releasing an acid and an alcohol that can be detected directly. This article reviews development, characterization and applications of organophosphorus hydrolase-based potentiometric, amperometric and optical biosensors.

Viscosity and binder composition effects on tyrosinase-based carbon paste electrode for detection of phenol and catechol.

The systematic study of the effect of binder viscosity on the sensitivity of a tyrosinase-based carbon paste electrode (CPE) biosensor for phenol and catechol is reported. Silicon oil binders with similar (polydimethylsiloxane) chemical composition were used to represent a wide range of viscosities (10-60 000 mPa s(-1) at 25 degrees C) while minimizing polarity effects. The highest response for both phenol and catechol was achieved using a silicon oil binder of intermediate viscosity (100 mPa s(-1)). The binder viscosity showed no appreciable effect on the direct oxidation of phenol and catechol using a plain CPE, suggesting the involvement of diffusion kinetics in the binder matrix for the enzyme-based CPE. The effect of the relative binder concentration in the carbon paste was measured over the range of 30-70%. Optimal results were obtained using 40% silicon oil. For comparison of the viscosity effects observed with the carbon paste electrode (CPE) containing silicon oil, other low and high viscosity mineral oils and paraffin waxes were also examined.

Principles of affinity-based biosensors.

Despite the amount of resources that have been invested by national and international academic, government, and commercial sectors to develop affinity-based biosensor products, little obvious success has been realized through commercialization of these devices for specific applications (such as the enzyme biosensors for blood glucose analysis). Nevertheless, the fastest growing area in the biosensors research literature continues to involve advances in affinity-based biosensors and biosensor-related methods. Numerous biosensor techniques have been reported that allow researchers to better study the kinetics, structure, and (solid/liquid) interface phenomena associated with protein-ligand binding interactions. In addition, potential application areas for which affinity-based biosensor techniques show promise include clinical/diagnostics, food processing, military/antiterrorism, and environmental monitoring. The design and structural features of these devices--composed of a biological affinity element interfaced to a signal transducer--primarily determine their operational characteristics. This paper, although not intended as a comprehensive review, will outline the principles of affinity biosensors with respect to potential application areas.

The intermediate filament protein consensus motif of helix 2B: its atomic structure and contribution to assembly.

Nearly all intermediate filament proteins exhibit a highly conserved amino acid motif (YRKLLEGEE) at the C-terminal end of their central alpha-helical rod domain. We have analyzed its contribution to the various stages of assembly by using truncated forms of Xenopus vimentin and mouse desmin, VimIAT and DesIAT, which terminate exactly before this motif, by comparing them with the wild-type and tailless proteins. It is surprising that in buffers of low ionic strength and high pH where the full-length proteins form tetramers, both VimIAT and DesIAT associated into various high molecular weight complexes. After initiation of assembly, both VimIAT and DesIAT aggregated into unit-length-type filaments, which rapidly longitudinally annealed to yield filaments of around 20 nm in diameter. Mass measurements by scanning transmission electron microscopy revealed that both VimIAT and DesIAT filaments contained considerably more subunits per cross-section than standard intermediate filaments. This indicated that the YRKLLEGEE-motif is crucial for the formation of authentic tetrameric complexes and also for the control of filament width, rather than elongation, during assembly. To determine the structure of the YRKLLEGEE domain, we grew crystals of peptides containing the last 28 amino acid residues of coil 2B, chimerically fused at its amino-terminal end to the 31 amino acid-long leucine zipper domain of the yeast transcription factor GCN4 to facilitate appropriate coiled-coil formation. The atomic structure shows that starting from Tyr400 the two helices gradually separate and that the coiled coil terminates with residue Glu405 while the downstream residues fold away from the coiled-coil axis.

Detection of low dose radiation induced DNA damage using temperature differential fluorescence assay.

A rapid and sensitive fluorescence assay for radiation-induced DNA damage is reported. Changes in temperature-induced strand separation in both calf thymus DNA and plasmid DNA (puc 19 plasmid from Escherichia coli) were measured after exposure to low doses of radiation. Exposures of between 0.004 and 1 Gy were measured with doses as low as 0.008 Gy yielding significant responses. The double-strand, sensitive dye PicoGreen was used as an indicator of DNA denaturation. Calibration plots indicate that fluorescence changes corresponding to amounts as low as 1 ng of double stranded DNA (10(6) copies for plasmid puc 19) are detected by this method.

Peer reviewed: update on environmental biosensors.

Scientific understanding and technological development are advancing, but commercialization, with a few exceptions, has been slow.

Thick-film electrochemical immunosensor based on stripping potentiometric detection of a metal ion label.

A disposable electrochemical immunosensor based on potentiometric stripping analysis (PSA) of a metal tracer and using an entirely on-chip assay format is demonstrated. Challenges associated with the adaptation of earlier stripping voltammetric immunoassays to an on-chip operation, and with meeting the demands of decentralized testing, have been addressed. These include the surface immobilization of the antibody, the replacement of mercury drop electrodes, elimination of the separation and oxygen-removal steps, and the use of quiescent 30-microL sample droplets. Human serum albumin (HSA) and anti-HSA antibody were used as a model system, while bismuth ion served as the metal label. The anti-HSA was immobilized onto the surface of a thick-film electrode, followed by a competition between the Bi-labeled analyte-tracer and the analyte (HSA) for the antibody binding sites. Upon removal of the unbound tracer, Bi3+ was released and detected by PSA. The dynamic concentration range for HSA (0.3-30 micrograms/mL) and the detection limit (0.2 microgram/mL, i.e., 90 fmol in the 30-microL sample) indicate that the greatly simplified protocol does not compromise the performance characteristics of stripping immunoassays. Consequently, this on-chip operation offers great promise for decentralized (clinical and environmental) applications.

Sol-gel-derived thick-film amperometric immunosensors.

Sol-gel processing is used for the first time for the preparation of electrochemical immunosensors. One-step sensor fabrication, based on the coupling of sol-gel and screen-printing technologies, is employed. A low-temperature cured ink is prepared by dispersion of rabbit immunoglobulin G (RIgG), graphite powder, and a binder in the sol-gel solution. The enzyme-labeled antibody can readily diffuse toward the encapsulated antigen, which retains its binding properties, and the association reaction is easily detected at the dispersed graphite surface. Use of anti-RIgG labeled with alkaline phosphatase, naphthyl phosphate as the substrate, and amperometric detection at +400 mV (vs Ag/AgCl) results in a low detection limit of 5 ng/mL (32 pM) for the solution antigen. Tailoring the porosity of the ceramic-carbon matrix can be used for tuning the assay performance. The high sensitivity, low cost, durability, and simplicity of the new single-use immunosensors make them well suited for various on-site applications.

Screen-printed voltammetric sensor for TNT.

Screen-printed carbon electrodes have been developed as disposable voltammetric sensors for 2,4,6-trinitrotoluene (TNT). Thick-film electrodes based on various conventional and modified inks have been compared for this task. The operation is based on placing the selected thick-film carbon sensor in the non-deaerated/quiescent sample and using a fast (<1 s) and sensitive square-wave voltammetric scan. Different experimental variables have been optimized to yield a detection limit of 200 ppb TNT and a wide linear range. The high selectivity, demonstrated in assays of various untreated environmental samples, is attributed to the facts that the reducible nitro group is rare in nature and that most electroactive organic compounds require higher potentials. The new single-use sensor strips should facilitate the on-site environmental screening of TNT.

Detection of 2,4-dichlorophenoxyacetic acid using a fluorescence immunoanalyzer.

A flow immunoassay method for the measurement of 2,4-dichlorophenoxyacetic acid (2,4-D) was developed. The competitive fluorescence immunoassay relies on the use of antibody- or antigen-coated poly(methyl methacrylate) particles (98 microns diameter) as a renewable solid phase. The assay exhibits a dynamic range of 0.1-100 micrograms l-1 using a monoclonal antibody or alternatively 10 micrograms l-1 to 10 mg l-1 using commercially available antiserum. The assay is demonstrated in buffered saline solution as well as in aquatic environmental media. The relative errors for the environmental matrices were similar to those for the buffer control. The precision of concentration values calculated at 1 mg l-1 (for the assay using antiserum) were +/- 0.28, +/- 0.27 and +/- 0.43 mg l-1 for the buffer, well water and river water matrices, respectively. The method shows cross-reactivity with compounds of closely related structure but little cross-reactivity with compounds dissimilar in structure to 2,4-D. The proposed automated competitive immunoassay method is rapid (between 7 and 15 min per assay), simple and potentially portable.

The secretory epithelial cells of the choroid plexus employ a novel kinesin-related protein.

The proteins of the kinesin superfamily (KIFs) are microtubule-based molecular motors whose functions include the transport of membrane-bound organelles. We have isolated the cDNA encoding a novel kinesin by reverse transcription and polymerase chain reaction using degenerate primers that flank the highly conserved motor domain. The deduced amino acid sequence of this protein shows considerable similarity to both KIF1A and KIF1B thus defining it as a new member of the monomeric KIF1/unc104 family. The C-terminal domain of KIF1D is the most divergent by comparison with the other members of the family, which supports the view that the tail region is responsible for conferring specificity on the interactions of these kinesins with their cargoes. In the adult rat brain KIF1D mRNA is expressed in neurons in the hippocampus and in the Purkinje cells of the cerebellum. However, the levels of KIF1D are particularly high in the choroid plexus which is a polarised epithelium that lines the lateral, third and fourth ventricles. The major function of the epithelial cells in the choroid plexus is to produce cerebrospinal fluid, which suggests that KIF1D plays an important role in their secretory function.

Characterization of disulfide crosslink formation of human vimentin at the dimer, tetramer, and intermediate filament levels.

We have investigated the structural interactions of individual molecules of human vimentin in the soluble state and in filaments. Oxidative crosslinking experiments were conducted with wild-type vimentin aimed at the single cysteine in the helical domain coil 2b, mutated cysteine-free vimentin, and derivatives engineered to carry cysteines in presumed d positions of the heptad amino acid repeats in coils 1a and 2b. We provide conclusive evidence that crosslinking of the cysteine 328 in wild-type vimentin, when in the filamentous or tetrameric forms, occurs outside of the coiled-coil dimer, i.e., between staggered dimer molecules. This occurs despite the close axial register of the dimers and contradicts previous deductions. The extent of crosslinking increases with temperature as well as with the concentration of the crosslinking reagent. We conclude therefore that the cysteines are not in an ideal position for crosslinking but that molecular motion is needed to enhance the reaction. The occurrence of collision complexes, which has been speculated in the literature, does not occur and cannot explain these results. Furthermore, using tailless vimentin with the corresponding mutations, we provide compelling evidence that in type III intermediate filament proteins exchange of individual chains between dimers occurs only if the proteins are incubated in urea at concentrations above 3 M. In 5 M urea, however, the exchange is completed within seconds. The same reaction occurs between human vimentin and mouse desmin at a comparable speed, indicating that both type III intermediate filament proteins have a high affinity for one another at the coiled-coil level.

Peer reviewed: environmental biosensors: a status report.

New instruments and methods being developed show promise for continuous, in situ monitoring of toxic compounds.

Truncation mutagenesis of the non-alpha-helical carboxyterminal tail domain of vimentin reveals contributions to cellular localization but not to filament assembly.

We have investigated the effect of stepwise truncating the carboxyterminal domain ("tail") of the intermediate filament (IF) protein vimentin of the clawed toad, Xenopus laevis, on filament assembly in vitro and, using cell transfection, in vivo and also on the cellular topology of the structures formed. All truncations examined, except the minimal one missing the last 11 amino acids which made the protein more sensitive to changes of ionic strength, did not significantly alter IF assembly in vitro, as judged by electron microscopy, viscometry and determination of viscoelastic properties with a laser-operated torsion pendulum. Stable transfections of vimentin-free mammalian cells with cDNAs encoding these mutations resulted at 28 degrees C, i.e. the permissive temperature for assembly of Xenopus vimentin, in the formation of extended IF bundle arrays. At 37 degrees C, however, the mutants lacking more than the last 35 amino acids could leave the cytoplasm and accumulated in the nucleus, indicating a certain topogenic element is located in the tail and directs cytoplasmic restriction in the wild-type protein although this does not form IFs under these conditions. Transfer to the nucleus is, however, abolished if the IF-consensus motif at the end of the rod domain is removed, suggesting that this part of the molecule also contributes to nuclear location. Similar results were obtained with human vimentin: While the rod entered the nucleus, headless vimentin, unable to form IFs, remained restricted to the cytoplasm owing to its tail domain. In contrast, tailless human vimentin and tailless mouse desmin, which are fully assembly-competent in vitro, both formed extensive IF arrays in the cytoplasm but did not accumulate in the nucleus. We conclude that in class III IF proteins stepwise deletions in the tail, while not considerably altering IF assembly in vitro, can change the topogenesis of IF proteins and structures in the living cell.

Detection of nicotinic receptor ligands with a light addressable potentiometric sensor.

The nicotinic acetylcholine receptor, purified from Torpedo electric organ, was coupled to a light addressable potentiometric sensor (LAPS) to form a LAPS-receptor biosensor. Receptor-ligand complexes containing biotin and urease were captured on a biotinylated nitrocellulose membrane via a streptavidin bridge and detected with a silicon-based sensor. Competition between biotinylated alpha-bungarotoxin and nonbiotinylated ligands formed the basis of this assay. This biosensor detected both agonists (acetylcholine, carbamylcholine, succinylcholine, suberyldicholine, and nicotine) and competitive antagonists (d-tubocurarine, alpha-bungarotoxin, and alpha-Naja toxin) of the receptor with affinities comparable to those obtained using radioactive ligand binding assays. Consistent with agonist-induced desensitization of the receptor, the LAPS-receptor biosensor reported a time-dependent increase in affinity for the agonist carbamylcholine as expected, but not for the antagonists.

Biosensors for environmental monitoring.

In this article we will outline several biosensor applications which may fill existing technology gaps in the area of environmental monitoring. The requirements for these environmental biosensors, as well as difficulties in commercialization, are also addressed.